-
2
-
-
0028853544
-
Principles of protein-protein recognition from structure to thermodynamics
-
Janin J. Principles of protein-protein recognition from structure to thermodynamics. Biochimie 1995;77:497-505.
-
(1995)
Biochimie
, vol.77
, pp. 497-505
-
-
Janin, J.1
-
3
-
-
84868129687
-
Towards a better understanding of the specificity of protein-protein interaction
-
Kysilka J, Vondrasek, J. Towards a better understanding of the specificity of protein-protein interaction. J Mol Recognit 2012;25:604-615.
-
(2012)
J Mol Recognit
, vol.25
, pp. 604-615
-
-
Kysilka, J.1
Vondrasek, J.2
-
4
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman K, Kern D. Dynamic personalities of proteins. Nature 2007;450:964-972.
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
5
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
Lange OF, Lakomek NA, Fares C, Schröder GF, Walter KFA, Becker S, Meiler J, Grubmueller H, Griesinger C, de Groot BL. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 2008;320:1471-1475.
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
Lakomek, N.A.2
Fares, C.3
Schröder, G.F.4
Walter, K.F.A.5
Becker, S.6
Meiler, J.7
Grubmueller, H.8
Griesinger, C.9
de Groot, B.L.10
-
6
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009;5:789-796.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
7
-
-
76649114676
-
Protein dynamics and conformational disorder in molecular recognition
-
Mittag T, Kay LE, Forman-Kay JD. Protein dynamics and conformational disorder in molecular recognition. J Mol Recognit 2010;23:105-116.
-
(2010)
J Mol Recognit
, vol.23
, pp. 105-116
-
-
Mittag, T.1
Kay, L.E.2
Forman-Kay, J.D.3
-
8
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: a matter of pre-exisiting populations
-
Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-exisiting populations. Protein Sci 2002;11:184-197.
-
(2002)
Protein Sci
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
9
-
-
0033056708
-
Folding funnels, binding funnels, and protein function
-
Tsai CJ, Kumar S, Ma B, Nussinov R. Folding funnels, binding funnels, and protein function. Protein Sci 1999;8:1181-1190.
-
(1999)
Protein Sci
, vol.8
, pp. 1181-1190
-
-
Tsai, C.J.1
Kumar, S.2
Ma, B.3
Nussinov, R.4
-
10
-
-
17844410707
-
The many faces of protease-protein inhibitor interaction
-
Otlewski J, Jelen F, Zakrzewska M, Oleksy A. The many faces of protease-protein inhibitor interaction. EMBO J 2005;24:1303-1310.
-
(2005)
EMBO J
, vol.24
, pp. 1303-1310
-
-
Otlewski, J.1
Jelen, F.2
Zakrzewska, M.3
Oleksy, A.4
-
11
-
-
0028914722
-
Structural basis of substrate specificity in the serine proteases
-
Perona JJ, Craik CS. Structural basis of substrate specificity in the serine proteases. Protein Sci 1995;4:337-360.
-
(1995)
Protein Sci
, vol.4
, pp. 337-360
-
-
Perona, J.J.1
Craik, C.S.2
-
12
-
-
44949142150
-
Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites
-
Schilling O, Overall CM. Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nat Biotechnol 2008;26:685-694.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 685-694
-
-
Schilling, O.1
Overall, C.M.2
-
13
-
-
79251491023
-
Current strategies for probing substrate specificity of proteases
-
Poreba M, Drag M. Current strategies for probing substrate specificity of proteases. Curr Med Chem 2010;17:3968-3995.
-
(2010)
Curr Med Chem
, vol.17
, pp. 3968-3995
-
-
Poreba, M.1
Drag, M.2
-
14
-
-
84869088814
-
Global identification of peptidase specificity by multiplex substrate profiling
-
O'Donoghue AJ, Eroy-Reveles AA, Knudsen GM, Ingram J, Zhou M, Statnekov JB, Greninger AL, Hostetter DR, Qu G, Maltby DA, Anderson MO, DeRisi JL, McKerrow JH, Burlingame AL, Craik CS. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods 2012;9:1095-1103.
-
(2012)
Nat Methods
, vol.9
, pp. 1095-1103
-
-
O'Donoghue, A.J.1
Eroy-Reveles, A.A.2
Knudsen, G.M.3
Ingram, J.4
Zhou, M.5
Statnekov, J.B.6
Greninger, A.L.7
Hostetter, D.R.8
Qu, G.9
Maltby, D.A.10
Anderson, M.O.11
DeRisi, J.L.12
McKerrow, J.H.13
Burlingame, A.L.14
Craik, C.S.15
-
15
-
-
84876935490
-
Cleavage entropy as quantitative measure of protease specificity
-
Fuchs JE, von Grafenstein S, Huber RG, Margreiter MA, Spitzer GM, Wallnoefer HG, Liedl KR. Cleavage entropy as quantitative measure of protease specificity. PLOS Comput Biol 2013;9:e1003007.
-
(2013)
PLOS Comput Biol
, vol.9
-
-
Fuchs, J.E.1
von Grafenstein, S.2
Huber, R.G.3
Margreiter, M.A.4
Spitzer, G.M.5
Wallnoefer, H.G.6
Liedl, K.R.7
-
16
-
-
69249100500
-
Human caspases: activation, specificity, and regulation
-
Pop C, Salvesen GS. Human caspases: activation, specificity, and regulation. J Biol Chem 2009;284:21777-21781.
-
(2009)
J Biol Chem
, vol.284
, pp. 21777-21781
-
-
Pop, C.1
Salvesen, G.S.2
-
17
-
-
0032575750
-
Caspases: enemies within
-
Thornberry NA, Lazebnik Y. Caspases: enemies within. Science 1998;281:1312-1316.
-
(1998)
Science
, vol.281
, pp. 1312-1316
-
-
Thornberry, N.A.1
Lazebnik, Y.2
-
18
-
-
0034641918
-
The biochemistry of apoptosis
-
Hengartner MO. The biochemistry of apoptosis. Nature 2000;407:770-776.
-
(2000)
Nature
, vol.407
, pp. 770-776
-
-
Hengartner, M.O.1
-
19
-
-
26444560960
-
Caspases: pharmacological manipulation of cell death
-
Lavrik IN, Golks A, Krammer PH. Caspases: pharmacological manipulation of cell death. J Clin Invest 2005;115:2665-2672.
-
(2005)
J Clin Invest
, vol.115
, pp. 2665-2672
-
-
Lavrik, I.N.1
Golks, A.2
Krammer, P.H.3
-
20
-
-
34547430973
-
Structural and functional definition of the specificity of a novel caspase-3 inhibitor, Ac-DNLD-CHO
-
Yoshimori A, Sakai J, Sunaga S, Kobayashi T, Takahashi S, Okita N, Takasawa R, Tanuma S. Structural and functional definition of the specificity of a novel caspase-3 inhibitor, Ac-DNLD-CHO. BMC Pharmacol 2007;7:8.
-
(2007)
BMC Pharmacol
, vol.7
, pp. 8
-
-
Yoshimori, A.1
Sakai, J.2
Sunaga, S.3
Kobayashi, T.4
Takahashi, S.5
Okita, N.6
Takasawa, R.7
Tanuma, S.8
-
21
-
-
10644282148
-
The protein structures that shape caspase activity, specificity, activation and inhibition
-
Fuentes-Prior P, Salvesen GS. The protein structures that shape caspase activity, specificity, activation and inhibition. Biochem J 2004;382:201-232.
-
(2004)
Biochem J
, vol.382
, pp. 201-232
-
-
Fuentes-Prior, P.1
Salvesen, G.S.2
-
22
-
-
33750690511
-
Role of loop bundle hydrogen bonds in the maturation and activity of (Pro)caspase-3
-
Feeney B, Pop C, Swartz P, Mattos C, Clark AC. Role of loop bundle hydrogen bonds in the maturation and activity of (Pro)caspase-3. Biochemistry 2006;45:13249-13263.
-
(2006)
Biochemistry
, vol.45
, pp. 13249-13263
-
-
Feeney, B.1
Pop, C.2
Swartz, P.3
Mattos, C.4
Clark, A.C.5
-
23
-
-
0035798361
-
Crystal Structure of a procaspase-7 zymogen: mechanisms of activation and substrate binding
-
Chai J, Wu Q, Shiozaki E, Srinivasula SM, Alnemri ES, Shi Y. Crystal Structure of a procaspase-7 zymogen: mechanisms of activation and substrate binding. Cell 2001;107:399-407.
-
(2001)
Cell
, vol.107
, pp. 399-407
-
-
Chai, J.1
Wu, Q.2
Shiozaki, E.3
Srinivasula, S.M.4
Alnemri, E.S.5
Shi, Y.6
-
24
-
-
0038306254
-
Conformational restrictions in the active site of unliganded human caspase-3
-
Ni CZ, Li C, Wu JC, Spada AP, Ely KR. Conformational restrictions in the active site of unliganded human caspase-3. J Mol Recognit 2003;16:121-124.
-
(2003)
J Mol Recognit
, vol.16
, pp. 121-124
-
-
Ni, C.Z.1
Li, C.2
Wu, J.C.3
Spada, A.P.4
Ely, K.R.5
-
25
-
-
69949145123
-
Conformational similarity in the activation of caspase-3 and -7 revealed by the unliganded and inhibited structures of caspase-7
-
Agniswamy J, Fang B, Weber IT. Conformational similarity in the activation of caspase-3 and -7 revealed by the unliganded and inhibited structures of caspase-7. Apoptosis 2009;14:1135-1144.
-
(2009)
Apoptosis
, vol.14
, pp. 1135-1144
-
-
Agniswamy, J.1
Fang, B.2
Weber, I.T.3
-
26
-
-
33748759801
-
Small-molecule activation of procaspase-3 to caspase-3 as a personalized anticancer strategy
-
Putt KS, Chen GW, Pearson JM, Sandhorst JS, Hoagland MS, Kwon JT, Hwang SK, Jin H, Churchwell MI, Cho MH, Doerge DR, Helferich WG, Hergenrother PJ. Small-molecule activation of procaspase-3 to caspase-3 as a personalized anticancer strategy. Nat Chem Biol 2006;2:543-550.
-
(2006)
Nat Chem Biol
, vol.2
, pp. 543-550
-
-
Putt, K.S.1
Chen, G.W.2
Pearson, J.M.3
Sandhorst, J.S.4
Hoagland, M.S.5
Kwon, J.T.6
Hwang, S.K.7
Jin, H.8
Churchwell, M.I.9
Cho, M.H.10
Doerge, D.R.11
Helferich, W.G.12
Hergenrother, P.J.13
-
27
-
-
80052307868
-
A bifunctional allosteric site in the dimer interface of procaspase-3
-
Schipper JL, MacKenzie SH, Sharma A, Clark AC. A bifunctional allosteric site in the dimer interface of procaspase-3. Biophys Chem 2011;159:100-109.
-
(2011)
Biophys Chem
, vol.159
, pp. 100-109
-
-
Schipper, J.L.1
MacKenzie, S.H.2
Sharma, A.3
Clark, A.C.4
-
28
-
-
0034095571
-
The structures of caspases-1, -3, -7 and -8 reveal the basis for substrate and inhibitor selectivity
-
Wei T, Fox T, Chambers SP, Sintchak JA, Coll JT, Golec JMC, Swenson L, Wilson KP, Charifson PS. The structures of caspases-1, -3, -7 and -8 reveal the basis for substrate and inhibitor selectivity. Chem Biol 2000;7:423-432.
-
(2000)
Chem Biol
, vol.7
, pp. 423-432
-
-
Wei, T.1
Fox, T.2
Chambers, S.P.3
Sintchak, J.A.4
Coll, J.T.5
Golec, J.M.C.6
Swenson, L.7
Wilson, K.P.8
Charifson, P.S.9
-
29
-
-
80052754179
-
Caspase-1 promiscuity is counterbalanced by rapid inactivation of processed enzyme
-
Walsh JG, Logue SE, Luethi AU, Martin SJ. Caspase-1 promiscuity is counterbalanced by rapid inactivation of processed enzyme. J Biol Chem 2011;286:32513-32524.
-
(2011)
J Biol Chem
, vol.286
, pp. 32513-32524
-
-
Walsh, J.G.1
Logue, S.E.2
Luethi, A.U.3
Martin, S.J.4
-
30
-
-
0030849093
-
A combinatorial approach defines specificities of members of the caspase family and granzyme B
-
Thornberry NA, Rano TA, Peterson EP, Rasper DM, Timkey T, Garcia-Calvo M, Houtzager VM, Nordstrom PA, Roy S, Vaillancourt JP, Chapman KT, Nicholson DW. A combinatorial approach defines specificities of members of the caspase family and granzyme B. J Biol Chem 1997;272:17907-17911.
-
(1997)
J Biol Chem
, vol.272
, pp. 17907-17911
-
-
Thornberry, N.A.1
Rano, T.A.2
Peterson, E.P.3
Rasper, D.M.4
Timkey, T.5
Garcia-Calvo, M.6
Houtzager, V.M.7
Nordstrom, P.A.8
Roy, S.9
Vaillancourt, J.P.10
Chapman, K.T.11
Nicholson, D.W.12
-
31
-
-
0034283578
-
Internally quenched fluorescent peptide substrates disclose the subsite preferences of human caspases 1, 3, 6, 7 and 8
-
Stennicke HR, Renatus M, Meldal M, Salvesen GS. Internally quenched fluorescent peptide substrates disclose the subsite preferences of human caspases 1, 3, 6, 7 and 8. Biochem J 2000;350:563-568.
-
(2000)
Biochem J
, vol.350
, pp. 563-568
-
-
Stennicke, H.R.1
Renatus, M.2
Meldal, M.3
Salvesen, G.S.4
-
32
-
-
69249206534
-
Evaluation of recombinant caspase specificity by competitive substrates
-
Benkova B, Lozanov V, Ivanov IP, Mitev, V. Evaluation of recombinant caspase specificity by competitive substrates. Anal Biochem 2009;394:68-74.
-
(2009)
Anal Biochem
, vol.394
, pp. 68-74
-
-
Benkova, B.1
Lozanov, V.2
Ivanov, I.P.3
Mitev, V.4
-
33
-
-
0030948457
-
Substrate specificities of caspase family proteases
-
Talanian RV, Quinlan C, Trautz S, Hackett MC, Mankovich JA, Banach D, Ghayur T, Brady KD, Wong WW. Substrate specificities of caspase family proteases. J Biol Chem 1997;272:9677-9682.
-
(1997)
J Biol Chem
, vol.272
, pp. 9677-9682
-
-
Talanian, R.V.1
Quinlan, C.2
Trautz, S.3
Hackett, M.C.4
Mankovich, J.A.5
Banach, D.6
Ghayur, T.7
Brady, K.D.8
Wong, W.W.9
-
34
-
-
32444434664
-
Caspases 3 and 7: key mediators of mitochondrial events of apoptosis
-
Lakhani SA, Masud A, Kuida K, Porter GA, Jr., Booth CJ, Mehal WZ, Inayat I, Flavell RA. Caspases 3 and 7: key mediators of mitochondrial events of apoptosis. Science 2006;311:847-851.
-
(2006)
Science
, vol.311
, pp. 847-851
-
-
Lakhani, S.A.1
Masud, A.2
Kuida, K.3
Porter Jr, G.A.4
Booth, C.J.5
Mehal, W.Z.6
Inayat, I.7
Flavell, R.A.8
-
35
-
-
0029956641
-
Decreased apoptosis in the brain and premature lethality in CPP32-deficient mice
-
Kuida K, Zheng TS, Na S, Kuan CY, Yang D, Karasuyama H, Rakic P, Flavell RA. Decreased apoptosis in the brain and premature lethality in CPP32-deficient mice. Nature 1996;384:368-372.
-
(1996)
Nature
, vol.384
, pp. 368-372
-
-
Kuida, K.1
Zheng, T.S.2
Na, S.3
Kuan, C.Y.4
Yang, D.5
Karasuyama, H.6
Rakic, P.7
Flavell, R.A.8
-
36
-
-
7744226465
-
Caspase-7 expanded function and intrinsic expression level underlies strain-specific brain phenotype of caspase-3-null mice
-
Houde C, Banks KG, Coulombe N, Rasper D, Grimm E, Roy S, Simpson EM, Nicholson DW. Caspase-7 expanded function and intrinsic expression level underlies strain-specific brain phenotype of caspase-3-null mice. J Neurosci 2004;24:9977-9984.
-
(2004)
J Neurosci
, vol.24
, pp. 9977-9984
-
-
Houde, C.1
Banks, K.G.2
Coulombe, N.3
Rasper, D.4
Grimm, E.5
Roy, S.6
Simpson, E.M.7
Nicholson, D.W.8
-
37
-
-
70449378957
-
Caspase substrates: easily caught in deep waters?
-
Demon D, van Damme P, Vandenberghe T, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P. Caspase substrates: easily caught in deep waters? Trends Biotechnol 2009;27:680-688.
-
(2009)
Trends Biotechnol
, vol.27
, pp. 680-688
-
-
Demon, D.1
van Damme, P.2
Vandenberghe, T.3
Vandekerckhove, J.4
Declercq, W.5
Gevaert, K.6
Vandenabeele, P.7
-
38
-
-
33947426526
-
The CASBAH: a searchable database of caspase substrates
-
Luethi AU, Martin SJ. The CASBAH: a searchable database of caspase substrates. Cell Death Differ 2007;14:641-650.
-
(2007)
Cell Death Differ
, vol.14
, pp. 641-650
-
-
Luethi, A.U.1
Martin, S.J.2
-
39
-
-
51349139607
-
Executioner caspase-3 and caspase-7 are functionally distinct proteases
-
Walsh JG, Cullen SP, Sheridan C, Luethi AU, Gerner C, Martin SJ. Executioner caspase-3 and caspase-7 are functionally distinct proteases. Proc Natl Acad Sci USA 2008;105:12815-12819.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 12815-12819
-
-
Walsh, J.G.1
Cullen, S.P.2
Sheridan, C.3
Luethi, A.U.4
Gerner, C.5
Martin, S.J.6
-
40
-
-
75149167437
-
Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 Versus caspase-3 specificity
-
Demon D, van Damme P, Vandenberghe T, Deceuninck A, van Durme J, Verspurten J, Helsens K, Impens F, Wejda M, Schymkowitz J, Rousseau F, Madder A, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P. Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 Versus caspase-3 specificity. Mol Cell Proteomics 2009;8:2700-2714.
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 2700-2714
-
-
Demon, D.1
van Damme, P.2
Vandenberghe, T.3
Deceuninck, A.4
van Durme, J.5
Verspurten, J.6
Helsens, K.7
Impens, F.8
Wejda, M.9
Schymkowitz, J.10
Rousseau, F.11
Madder, A.12
Vandekerckhove, J.13
Declercq, W.14
Gevaert, K.15
Vandenabeele, P.16
-
41
-
-
34548407043
-
Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis
-
Agniswamy J, Fang B, Weber IT. Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis. FEBS J 2007;274:4752-4765.
-
(2007)
FEBS J
, vol.274
, pp. 4752-4765
-
-
Agniswamy, J.1
Fang, B.2
Weber, I.T.3
-
42
-
-
79959461070
-
Caspase substrates and cellular remodeling
-
Crawford ED, Wells JA. Caspase substrates and cellular remodeling. Annu Rev Biochem 2011;80:1055-1087.
-
(2011)
Annu Rev Biochem
, vol.80
, pp. 1055-1087
-
-
Crawford, E.D.1
Wells, J.A.2
-
43
-
-
52649141086
-
Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini
-
Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 2008;134:866-876.
-
(2008)
Cell
, vol.134
, pp. 866-876
-
-
Mahrus, S.1
Trinidad, J.C.2
Barkan, D.T.3
Sali, A.4
Burlingame, A.L.5
Wells, J.A.6
-
44
-
-
84871967410
-
SVM-based prediction of caspase substrate cleavage sites
-
Wee LJ, Tan TW, Ranganathan, S. SVM-based prediction of caspase substrate cleavage sites. BMC Bioinformatics 2010;7 (Suppl 5):S14.
-
(2010)
BMC Bioinformatics
, vol.7
, Issue.SUPPL 5
-
-
Wee, L.J.1
Tan, T.W.2
Ranganathan, S.3
-
45
-
-
77954481626
-
Prediction of protease substrates using sequence and structure features
-
Barkan DT, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A. Prediction of protease substrates using sequence and structure features. Bioinformatics 2010;26:1714-1722.
-
(2010)
Bioinformatics
, vol.26
, pp. 1714-1722
-
-
Barkan, D.T.1
Hostetter, D.R.2
Mahrus, S.3
Pieper, U.4
Wells, J.A.5
Craik, C.S.6
Sali, A.7
-
46
-
-
77951972791
-
Cascleave: towards more accurate prediction of caspase substrate cleavage sites
-
Song J, Tan H, Shen H, Mahmood K, Boyd SE, Webb GI, Akutsu T, Whisstock JC. Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics 2010;26:752-760.
-
(2010)
Bioinformatics
, vol.26
, pp. 752-760
-
-
Song, J.1
Tan, H.2
Shen, H.3
Mahmood, K.4
Boyd, S.E.5
Webb, G.I.6
Akutsu, T.7
Whisstock, J.C.8
-
47
-
-
80052936907
-
Exploiting differences in caspase-2 and -3 S2 subsites for selectivity: structure-based design, solid-phase synthesis and in vitro activity of novel substrate-based caspase-2 inhibitors
-
Maillard MC, Brookfield FA, Courtney SM, Eustache FM, Gemkow MJ, Handel RK, Johnson LC, Johnson PD, Kerry MA, Krieger F, Meniconi M.; Munoz-Sanjuan I, Palfrey JJ, Park H, Schaertl S, Taylor MG, Weddell D, Dominguez C. Exploiting differences in caspase-2 and -3 S2 subsites for selectivity: structure-based design, solid-phase synthesis and in vitro activity of novel substrate-based caspase-2 inhibitors. Bioorg Med Chem 2011;19:5833-5851.
-
(2011)
Bioorg Med Chem
, vol.19
, pp. 5833-5851
-
-
Maillard, M.C.1
Brookfield, F.A.2
Courtney, S.M.3
Eustache, F.M.4
Gemkow, M.J.5
Handel, R.K.6
Johnson, L.C.7
Johnson, P.D.8
Kerry, M.A.9
Krieger, F.10
Meniconi, M.11
Munoz-Sanjuan, I.12
Palfrey, J.J.13
Park, H.14
Schaertl, S.15
Taylor, M.G.16
Weddell, D.17
Dominguez, C.18
-
48
-
-
2642514073
-
A novel method for evaluation and screening of caspase inhibitory peptides by the amino acid positional fitness score
-
Yoshimori A, Takasawa R, Tanuma S. A novel method for evaluation and screening of caspase inhibitory peptides by the amino acid positional fitness score. BMC Pharmacol 2004;4:7.
-
(2004)
BMC Pharmacol
, vol.4
, pp. 7
-
-
Yoshimori, A.1
Takasawa, R.2
Tanuma, S.3
-
49
-
-
53849142861
-
Structural basis for executioner caspase recognition of P5 position in substrates
-
Fu G, Chumanevich AA, Agniswamy J, Fang B, Harrison RW, Weber IT. Structural basis for executioner caspase recognition of P5 position in substrates. Apoptosis 2008;13:1291-1302.
-
(2008)
Apoptosis
, vol.13
, pp. 1291-1302
-
-
Fu, G.1
Chumanevich, A.A.2
Agniswamy, J.3
Fang, B.4
Harrison, R.W.5
Weber, I.T.6
-
50
-
-
67349217364
-
Caspase-3 binds diverse P4 residues in peptides as revealed by crystallographic and structural modeling
-
Fang B, Fu G, Agniswamy J, Harrison RW, Weber IT. Caspase-3 binds diverse P4 residues in peptides as revealed by crystallographic and structural modeling. Apoptosis 2009;14:741-752.
-
(2009)
Apoptosis
, vol.14
, pp. 741-752
-
-
Fang, B.1
Fu, G.2
Agniswamy, J.3
Harrison, R.W.4
Weber, I.T.5
-
51
-
-
84860995211
-
Exploring protein dynamics space: the dynasome as the missing link between protein structure and function
-
Hensen U, Meyer T, Haas J, Rex R, Vriend G, Grubmueller, H. Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. PLOS One 2012;7:e33931.
-
(2012)
PLOS One
, vol.7
-
-
Hensen, U.1
Meyer, T.2
Haas, J.3
Rex, R.4
Vriend, G.5
Grubmueller, H.6
-
52
-
-
2542598482
-
Molecular dynamics simulations of structural changes during procaspase 3 activation
-
Piana S, Rothlisberger U. Molecular dynamics simulations of structural changes during procaspase 3 activation. Proteins 2004;55:932-941.
-
(2004)
Proteins
, vol.55
, pp. 932-941
-
-
Piana, S.1
Rothlisberger, U.2
-
53
-
-
18844365441
-
Folding pathways for initiator and effector procaspases from computer simulations
-
Piana S, Taylor Z, Rothlisberger, U. Folding pathways for initiator and effector procaspases from computer simulations. Proteins 2005;59:765-772.
-
(2005)
Proteins
, vol.59
, pp. 765-772
-
-
Piana, S.1
Taylor, Z.2
Rothlisberger, U.3
-
55
-
-
84863667542
-
Allosteric modulation of caspase 3 through mutagenesis
-
Walters J, Schipper WL, Swartz P, Mattos C, Clar AC, Allosteric modulation of caspase 3 through mutagenesis. Biosci Rep 2012;32:401-411.
-
(2012)
Biosci Rep
, vol.32
, pp. 401-411
-
-
Walters, J.1
Schipper, W.L.2
Swartz, P.3
Mattos, C.4
Clar, A.C.5
-
56
-
-
84864549316
-
FLIM-FRET imaging of caspase-3 activitity in live cells using pair of red fluorescent proteins
-
Savitsky AP, Rusanov AL, Zherdeva VV, Gorodnichewa TV, Khrenova MG, Nemukhin AV. FLIM-FRET imaging of caspase-3 activitity in live cells using pair of red fluorescent proteins. Theranostics 2012;2:215-226.
-
(2012)
Theranostics
, vol.2
, pp. 215-226
-
-
Savitsky, A.P.1
Rusanov, A.L.2
Zherdeva, V.V.3
Gorodnichewa, T.V.4
Khrenova, M.G.5
Nemukhin, A.V.6
-
57
-
-
84859426282
-
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors
-
Rawlings ND, Barrett AJ, Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 2012;40:D343-D350.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Rawlings, N.D.1
Barrett, A.J.2
Bateman, A.3
-
58
-
-
15844393657
-
The three-dimensional structure of apopain/CPP32, a key mediator of apoptosis
-
Rotonda J, Nicholson DW, Fazil KM, Gallant M, Gareau Y, Labelle M, Peterson EP, Rasper DM, Ruel R, Vaillancourt JP, Thornberry NA, Becker JW. The three-dimensional structure of apopain/CPP32, a key mediator of apoptosis. Nat Struct Biol 1993;3:619-625.
-
(1993)
Nat Struct Biol
, vol.3
, pp. 619-625
-
-
Rotonda, J.1
Nicholson, D.W.2
Fazil, K.M.3
Gallant, M.4
Gareau, Y.5
Labelle, M.6
Peterson, E.P.7
Rasper, D.M.8
Ruel, R.9
Vaillancourt, J.P.10
Thornberry, N.A.11
Becker, J.W.12
-
61
-
-
65249157397
-
Protonate 3D: assignment of ionization states and hydrogen coordinates to macromolecular structures
-
Labute P. Protonate 3D: assignment of ionization states and hydrogen coordinates to macromolecular structures. Proteins 2009;75:187-205.
-
(2009)
Proteins
, vol.75
, pp. 187-205
-
-
Labute, P.1
-
62
-
-
58049201323
-
-
San Francisco, CA: University of California;
-
Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Crowley M, Walker RC, Zhang W, Merz KM, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Mathews DH, Seetin MG, Sagui C, Babin V, Kollman PA. AMBER 10. San Francisco, CA: University of California; 2008.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham TE, I.I.I.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossváry, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
63
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura J, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Impey, R.W.4
Klein, M.L.5
-
64
-
-
77953513118
-
Improved side-chain torsion potentials for the Amber ff99SB protein force field
-
Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 2010;78:1950-1958.
-
(2010)
Proteins
, vol.78
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Piana, S.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
Shaw, D.E.7
-
65
-
-
33846823909
-
Particle mesh Ewald: an N*log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen, L. Particle mesh Ewald: an N*log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
66
-
-
77952914469
-
Stabilizing of a globular protein by a highly complex water network: a molecular dynamics study on factor Xa
-
Wallnoefer HG, Handschuh S, Liedl KR, Fox T. Stabilizing of a globular protein by a highly complex water network: a molecular dynamics study on factor Xa. J Phys Chem B 2010;114:7405-7412.
-
(2010)
J Phys Chem B
, vol.114
, pp. 7405-7412
-
-
Wallnoefer, H.G.1
Handschuh, S.2
Liedl, K.R.3
Fox, T.4
-
67
-
-
36749113534
-
Generalized Langevin equation approach for atom-solid-surface scattering-general formulation for classical scattering off harmonic solids
-
Adelman SA, Doll JD. Generalized Langevin equation approach for atom-solid-surface scattering-general formulation for classical scattering off harmonic solids. J Chem Phys 1976;64:2375-2388.
-
(1976)
J Chem Phys
, vol.64
, pp. 2375-2388
-
-
Adelman, S.A.1
Doll, J.D.2
-
68
-
-
46149128394
-
Molecular dynamics simulation of rigid molecules
-
Ciccotti G, Ryckaert JP. Molecular dynamics simulation of rigid molecules. Comput Phys Rep 1986;4:345-392.
-
(1986)
Comput Phys Rep
, vol.4
, pp. 345-392
-
-
Ciccotti, G.1
Ryckaert, J.P.2
-
69
-
-
0030729481
-
Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold
-
Perona JJ, Craik CS. Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold. J Biol Chem 1997;272:29987-29990.
-
(1997)
J Biol Chem
, vol.272
, pp. 29987-29990
-
-
Perona, J.J.1
Craik, C.S.2
-
70
-
-
0026520387
-
Converting trypsin to chymotrypsin-the role of surface loops
-
Hedstrom L, Szilagyi L, Rutter WJ. Converting trypsin to chymotrypsin-the role of surface loops. Science 1992;255:1249-1253.
-
(1992)
Science
, vol.255
, pp. 1249-1253
-
-
Hedstrom, L.1
Szilagyi, L.2
Rutter, W.J.3
-
71
-
-
23244458844
-
Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant
-
Ma W, Tang C, Lai L. Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant. Biophys J 2005;89:1183-1193.
-
(2005)
Biophys J
, vol.89
, pp. 1183-1193
-
-
Ma, W.1
Tang, C.2
Lai, L.3
-
72
-
-
71549124315
-
Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action
-
Gaspari Z, Varnai P, Szappanos B, Perczel A. Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action. FEBS Lett 2010;584:203-206.
-
(2010)
FEBS Lett
, vol.584
, pp. 203-206
-
-
Gaspari, Z.1
Varnai, P.2
Szappanos, B.3
Perczel, A.4
-
73
-
-
77956279561
-
NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation
-
Lechtenberg BC, Johnson DJ, Freund SM, Huntington JA. NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation. Proc Natl Acad Sci USA 2010;107:14087-14092.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 14087-14092
-
-
Lechtenberg, B.C.1
Johnson, D.J.2
Freund, S.M.3
Huntington, J.A.4
-
75
-
-
0029128015
-
Functional linkage between the active site of alpha-lytic protease and distant regions of structure: scanning alanine mutagenesis of a surface loop affects activity and substrate specificity
-
Mace JE, Wilk BJ, Agard DA. Functional linkage between the active site of alpha-lytic protease and distant regions of structure: scanning alanine mutagenesis of a surface loop affects activity and substrate specificity. J Mol Biol 1995;251:116-134.
-
(1995)
J Mol Biol
, vol.251
, pp. 116-134
-
-
Mace, J.E.1
Wilk, B.J.2
Agard, D.A.3
-
76
-
-
0029610386
-
Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity
-
Mace JE, Agard DA. Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity. J Mol Biol 1995;254:720-736.
-
(1995)
J Mol Biol
, vol.254
, pp. 720-736
-
-
Mace, J.E.1
Agard, D.A.2
-
77
-
-
80051739212
-
Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope
-
Ozen A, Haliloglu T, Schiffer CA. Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope. J Mol Biol 2011;410:726-744.
-
(2011)
J Mol Biol
, vol.410
, pp. 726-744
-
-
Ozen, A.1
Haliloglu, T.2
Schiffer, C.A.3
-
78
-
-
0033543577
-
Altered flexibility in the substrate-binding site of related native and engineered high-alkaline Bacillus subtilisins
-
Mulder FA, Schipper D, Bott R, Boelens R. Altered flexibility in the substrate-binding site of related native and engineered high-alkaline Bacillus subtilisins. J Mol Biol 1999;292:111-123.
-
(1999)
J Mol Biol
, vol.292
, pp. 111-123
-
-
Mulder, F.A.1
Schipper, D.2
Bott, R.3
Boelens, R.4
-
79
-
-
77955037998
-
Backbone flexibility controls the activity and specificity of a protein-protein interface: specificity in snake venom metalloproteases
-
Wallnoefer HG, Lingott T, Gutierrez JM, Merfort I, Liedl KR. Backbone flexibility controls the activity and specificity of a protein-protein interface: specificity in snake venom metalloproteases. J Am Chem Soc 2010;132:10330-10337.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 10330-10337
-
-
Wallnoefer, H.G.1
Lingott, T.2
Gutierrez, J.M.3
Merfort, I.4
Liedl, K.R.5
-
81
-
-
0036882394
-
Serine protease mechanism and specificity
-
Hedstrom L. Serine protease mechanism and specificity. Chem Rev 2002;102:4501-4524.
-
(2002)
Chem Rev
, vol.102
, pp. 4501-4524
-
-
Hedstrom, L.1
|